Strategies for dereplication of natural compounds using high-resolution tandem mass spectrometry

Tobias Kind, Oliver Fiehn

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


Complete structural elucidation of natural products is commonly performed by nuclear magnetic resonance spectroscopy (NMR), but annotating compounds to most likely structures using high-resolution tandem mass spectrometry is a faster and feasible first step. The CASMI contest 2016 (Critical Assessment of Small Molecule Identification) provided spectra of eighteen compounds for the best manual structure identification in the natural products category. High resolution precursor and tandem mass spectra (MS/MS) were available to characterize the compounds. We used the Seven Golden Rules, Sirius2 and MS-FINDER software for determination of molecular formulas, and then we queried the formulas in different natural product databases including DNP, UNPD, ChemSpider and REAXYS to obtain molecular structures. We used different in-silico fragmentation tools including CFM-ID, CSI:FingerID and MS-FINDER to rank these compounds. Additional neutral losses and product ion peaks were manually investigated. This manual and time consuming approach allowed for the correct dereplication of thirteen of the eighteen natural products.

Original languageEnglish (US)
JournalPhytochemistry Letters
StateAccepted/In press - Jul 15 2016


  • Dereplication
  • Natural products
  • Seven Golden Rules
  • Tandem mass spectra

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Agronomy and Crop Science
  • Plant Science


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